Related papers: Prefix-free parsing for merging big BWTs

Large-scale Transformer models have significantly promoted the recent development of natural language processing applications. However, little effort has been made to unify the effective models. In this paper, driven by providing a new set…

Federated learning has attracted growing interest as it preserves the clients' privacy. As a variant of federated learning, federated transfer learning utilizes the knowledge from similar tasks and thus has also been intensively studied.…

Set queries are fundamental operations in computer systems and applications.This paper addresses the fundamental problem of designing a probabilistic data structure that can quickly process set queries using a small amount of memory. We…

Gaussian processes (GPs) are crucial in machine learning for quantifying uncertainty in predictions. However, their associated covariance matrices, defined by kernel functions, are typically dense and large-scale, posing significant…

Many NLP models operate over sequences of subword tokens produced by hand-crafted tokenization rules and heuristic subword induction algorithms. A simple universal alternative is to represent every computerized text as a sequence of bytes…

We present a general framework, the coupled compound Poisson factorization (CCPF), to capture the missing-data mechanism in extremely sparse data sets by coupling a hierarchical Poisson factorization with an arbitrary data-generating model.…

In recent years, the focus of bioinformatics research has moved from individual sequences to collections of sequences. Given the fundamental role of the Burrows-Wheeler Transform (BWT) in string processing, a number of dedicated tools have…

Machine translation systems achieve near human-level performance on some languages, yet their effectiveness strongly relies on the availability of large amounts of parallel sentences, which hinders their applicability to the majority of…

Suffix trees are one of the most versatile data structures in stringology, with many applications in bioinformatics. Their main drawback is their size, which can be tens of times larger than the input sequence. Much effort has been put into…

Modern genomic analyses increasingly rely on pangenomes, that is, representations of the genome of entire populations. The simplest representation of a pangenome is a set of individual genome sequences. Compared to e.g. sequence graphs,…

Fine-tuning a pretrained transformer for a downstream task has become a standard method in NLP in the last few years. While the results from these models are impressive, applying them can be extremely computationally expensive, as is…

The Breadth First Search (BFS) algorithm is the foundation and building block of many higher graph-based operations such as spanning trees, shortest paths and betweenness centrality. The importance of this algorithm increases each day due…

A standard format used for storing the output of high-throughput sequencing experiments is the FASTQ format. It comprises three main components: (i) headers, (ii) bases (nucleotide sequences), and (iii) quality scores. FASTQ files are…

Federated Bayesian neural networks require fixing a prior on the model parameters together with a likelihood. Eliciting meaningful priors on the weight space of modern overparameterized models is notoriously difficult, and misspecification…

For years the model performance in machine learning obeyed a power-law relationship with the model size. For the consideration of parameter efficiency, recent studies focus on increasing model depth rather than width to achieve better…

The Burrows-Wheeler-Transform (BWT), a reversible string transformation, is one of the fundamental components of many current data structures in string processing. It is central in data compression, as well as in efficient query algorithms…

Parameter-efficient tuning aims to mitigate the large memory requirements of adapting pretrained language models for downstream tasks. For example, one popular method, prefix-tuning, prepends trainable tokens to sequences while freezing the…

Many graph problems were first shown to be fixed-parameter tractable using the results of Robertson and Seymour on graph minors. We show that the combination of finite, computable, obstruction sets and efficient order tests is not just one…

In the multi-cell multiuser multi-input multi-output (MU-MIMO) systems, fractional programming (FP) has demonstrated considerable effectiveness in optimizing beamforming vectors, yet it suffers from high computational complexity. Recent…

Fine-tuning large pre-trained language models on various downstream tasks with whole parameters is prohibitively expensive. Hence, Parameter-efficient fine-tuning has attracted attention that only optimizes a few task-specific parameters…